I just had a problem with my seller on ebay, has this ever happened to you???

It is likely that the confirmation letter that you got was generated from an auto-responder. The same letter goes out automatically to all of their customers. It does not mean that they will not except your money order. If they made arrangements with you individually for the money order payment, it is likely that they will still honor this arrangement. If you are unsure, just write back and ask them.